From chemistry-request@server.ccl.net  Sun Jul  9 19:45:45 2000
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Date: Sun, 09 Jul 2000 19:45:49 -0400
From: AHMED MOHAMED EL-SHAFEI <amelsha@unity.ncsu.edu>
Organization: NCSU/College of Textiles
To: chemistry@ccl.net
Subject: Fortran Compiler for IRIX 6.2 

Dear All,
Does any one know of any fortran Compiler web site for IRIX 6.2  free?
I was trying to install a fortran compiler  to get G94 running on a
silicon graphics machine, but I could not find any available free
downloadable Fortran Compiler!
I appreciated your help in advance.
Ahmed





From chemistry-request@server.ccl.net  Sun Jul  9 11:57:11 2000
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From: "Li Zhenhua" <lbbg123@yahoo.com>
To: "=?gb2312?B?1cW12A==?=" <zkcfx@263.net>, "CCL" <chemistry@ccl.net>
References: <39681D5D.04487@mta1>
Subject: Re: CCL:help on PM3 in g98 optimization 
Date: Sun, 9 Jul 2000 23:56:14 +0800
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Just yesterday, I met the same problem too. But after I rewrite geometry
into z-matrix, and optimize with opt=z-matrix, it is OK. I don't know why.
And we find that if we optimize the same cartissan geometry with methods
other than semi-empirical methods, it is also OK.


----- Original Message -----
From: "ÕÅµŲ" <zkcfx@263.net>
To: <chemistry@ccl.net>
Sent: Sunday, July 09, 2000 2:36 PM
Subject: CCL:help on PM3 in g98 optimization


>
> Dear cclers:
>      when I use PM3 to do  optimization using g98(use internal
coordinate),
> there is often an incomplete coordinate error,how I avoid this.
>
> _____________________________________________
> http://www.263.net http://fsurvey.cnnic.net.cn/survey/index.html
>

__________________________________________________
Do You Yahoo!?
Talk to your friends online with Yahoo! Messenger.
http://im.yahoo.com



From chemistry-request@server.ccl.net  Mon Jul 10 02:59:36 2000
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Date: Mon, 10 Jul 2000 16:58:40 +1000 (EST)
From: Kim Branson <bra369@pp.molsci.csiro.au>
To: chemistry@ccl.net
Subject: Compiling DOCK 4.01
In-Reply-To: <395C634A.5E8B38@nibsc.ac.uk>
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Hi all,

Has anyone out there managed to compile dock for any other platform than
SGI, i'm currently trying to build it for linux and later Windoze NT and
Solaris.

The current linux build fails at the linking step using gcc and g77.

Thanks

Kim Branson

Biomolecular Research Institute
343 Royal Parade
Parkvile
Victoria
Australia



From chemistry-request@server.ccl.net  Mon Jul 10 06:26:30 2000
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From: Luigi Cavallo <cavallo@chemistry.unina.it>
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Subject: coordinates of DMPC bilayer
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   Dear all,

I am looking for coordinates of a bilayer of DMPC for use in MD
simulations, and eventually parameters to be used with GROMOS.

Thanx in advance,

gg

--------------------------------------------------------------------------
| Dr. Luigi Cavallo                                Dept. of Chemistry    |
| Ph:  ++39-81-2536635                             Univ. of Naples       |
| Fax: ++39-81-5527771                             Via Mezzocannone 4    |
| Email cavallo@chemistry.unina.it                 I-80134 Napoli, ITALY |
--------------------------------------------------------------------------



From chemistry-request@server.ccl.net  Sun Jul  9 23:39:47 2000
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Date: Mon, 10 Jul 2000 14:18:50 +1000
To: chemistry@ccl.net
From: Adnan Hazar <Adnan.Hazar@students.vu.edu.au>
Subject: missing parameters - AMBER
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Dear All,

I would greatly appreciate any help to find a data set (preferably more
recent then Cornell et al. 1995) or the individual values for the following
missing parameters. I have already done a thorough search on the net, not
much luck. I am using HyperChem 4.5 for conformational search.

missing AMBER parameters:
CT-OS-C
CT-OS-C-N
CT-OS-C-O
OS-C
OS-C-N
OS-C-O
OS-CT-C

any pointers or individual values I'd be very happy.
many thanks in advance

Adnan




From chemistry-request@server.ccl.net  Mon Jul 10 07:05:47 2000
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From: Ascanio DiPippo <ascanio@salve.edu>
To: chemistry@ccl.net
Subject: G94 (Gaussian 94 manual)
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Colleagues,
	A short time ago, someone was looking for a copy(or access
to)  the manual for GAUSSIAN 94 User's Reference manual) I have access to
Revision D.1 and higher. Please contact me at this e-mail address in the
next week or so as I will be attending a Gordon Conference at this Salve
Regina University site in Newport, R.I 

Rocco M.   



From chemistry-request@server.ccl.net  Mon Jul 10 11:33:17 2000
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Date: Mon, 10 Jul 2000 11:31:15 -0400
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: color prediction
To: "'CCL'" <chemistry@ccl.net>
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I didn't get as much response to this as I'd like--I still don't have a
procedure for obtaining a complete spectrum (intensity vs. wavelength).  But
several people have asked for a summary of the responses, so here they are:

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com


==============================
> 1. What level of theory is needed to get accurate electronic excitation
> energies?  I suppose this differs for organic and inorganic chromophores.

[from Huub van Dam]
To answer question 1 this question should be viewed in the light of
question 3. I.e. it is not enough to have a way of finding an accurate
excitation energy for just 1 excitation. You need an accurate way to
calculate the entire visible spectrum. Traditionally selected CI methods
have been used to calculate spectra, but they can be costly. To calculate
spectra response methods are quite suitable. In this category the TD-DFT
methods seem to be doing a good job nowadays. (Remember you need the
intensities as well as the energies).

[from John McKelvey]
For calculations of Lmax, for example, one could try the INDO/1S
method of Zerner, or even ab initio mmethods, and perhaps get reasonable
trends.  The quality of the trends can be _significantly_ affected by
geometry quality:6-31G*/b3lyp>6-31G*/blyp>3-21g/HF>am1>>pm3>>macromodel.


=========================
> 2. Is the electronic excitation energy pretty much equal to lambda-max,
> after the usual unit conversions?  Or do factors like vibrational
coupling
> come into play in a big way?

[from Huub van Dam]
Normally the vibrational motion should not have a big effect on
the electronic excitation energies.

=========================
> 3. To predict color you would need the entire absorption-vs.-wavelength
> plot, not just the lambda-max.  How does one get that?

[from John McKelvey]
Now, to get the _spectrum_ correct, one needs the correlation between
experiment and theory for Lmax to have slope=1 and intercept to be 0.
Significant recalibration work needs to be done.  [I've done this
before, and am currently a consultant in exactly this area.] My goal is
to reproduce the total spectrum from Lmax, oscillator strength,
band-width, and extinction coefficient. Non-trivial, but fun for me.]
Vibrational effects play a role, and have to be taken into account.

========================
> 4. Once one has such a plot, how does one convert into a perceived color?
> How does this interact with lighting conditions?

[from Huub van Dam]
The lighting conditions shouldn't be too difficult. The
perceived color is caused by the light that reflects from the pigment.  The
reflected light is the incoming light minus what is absorbed by the
pigment. A more interesting question is how do you simulate the spectrum
you calculated on a RGB screen. To answer this question you need to find
more about the human eye, like what are the 3 main frequencies it can
absorb and how strongly is each frequency being absorbed.
Another point which is probably not too important is that sometimes the
environment can actually change the color of a pigment. Most industries
will try to avoid making pigments like that but one has to be aware that
occasionally a pigment that looks okay as a powder can look different
embedded in a polymer say. So try your approach first on a few well known
pigments.

[from Malcolm Gillies]
I'm not sure how much you already know, but for a reasonable first
approximation, just multiply the absorption spectrum with the power
spectrum of your illuminant, and then multiply against each CIE standard
observer sensitivity curve for the three primaries and integrate.
This will give you the CIE XYZ values for the particular lighting
condition, which you can convert into any other colourspace you like
(RGB values for viewing on a computer, for instance).
The following URLs might be useful:
    Poynton's Color FAQ
    http://www.inforamp.net/~poynton/notes/colour_and_gamma/ColorFAQ.html
    CIE COLORIMETRY TABLES
    http://www.hike.te.chiba-u.ac.jp/ikeda/CIE/table/intro.html
    efg's colour reference library
    http://www.efg2.com/lab/library/Color.htm






From chemistry-request@server.ccl.net  Mon Jul 10 04:29:58 2000
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Sender: mathieu@ripault.cea.fr
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Date: Mon, 10 Jul 2000 10:07:56 +0200
From: Didier MATHIEU <mathieu@ripault.cea.fr>
Organization: CEA
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To: chemistry@ccl.net
Subject: Specific Buckingham parameters in Tinker
Content-Type: multipart/alternative;
 boundary="------------30F01F00174DEB9A75161471"


--------------30F01F00174DEB9A75161471
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Hello,

As a first step in the modelling of a family of organic crystals, I
consider using the simple Buckingham potential of Gavezzotti and
Filippini (in: Computational Approaches in Supramolecular Chemistry,
G. Wipff, ed. Kluwer, pp. 51-62 (1994)).
However, the A,B,C parameters in the expression E=Aexp(-BR)-C/R^6 do not
obey the usual combinations rules.
On the other hand, it seems that the Tinker program I use does expect
such rules.
Is it nonetheless possible to specify independent A,B,C parameters for
each atom pair to the program, or is it necessary to modify the programs
in order to introduce the extra degree of freedom required ?

Sincerely yours.

--
Didier MATHIEU
CEA - Le Ripault, BP 16
37260 Monts (France)
Tel. 33(0)2.47.34.41.85



--------------30F01F00174DEB9A75161471
Content-Type: text/html; charset=us-ascii
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Hello,
<p>As a first step in the modelling of a family of organic crystals, I
consider using the simple Buckingham potential of Gavezzotti and Filippini
(in: Computational Approaches in Supramolecular Chemistry, G.&nbsp;Wipff,
ed. Kluwer, pp. 51-62 (1994)).
<br>However, the A,B,C parameters in the expression E=Aexp(-BR)-C/R^6 do
not obey the usual combinations rules.
<br>On the other hand, it seems that the Tinker program I use does expect
such rules.
<br>Is it nonetheless possible to specify independent A,B,C parameters
for each atom pair to the program, or is it necessary to modify the programs
in order to introduce the extra degree of freedom required&nbsp;?
<p>Sincerely yours.
<pre>--&nbsp;
Didier MATHIEU
CEA - Le Ripault, BP 16
37260 Monts (France)
Tel. 33(0)2.47.34.41.85</pre>
&nbsp;</html>

--------------30F01F00174DEB9A75161471--



From chemistry-request@server.ccl.net  Mon Jul 10 11:47:18 2000
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Date: Mon, 10 Jul 2000 13:34:57 -0300
From: Eduardo Hollauer <edu@kabir.gqt.uff.br>
Message-Id: <200007101634.NAA05487@kabir.gqt.uff.br>
To: CHEMISTRY@ccl.net



        Dear CCL Friends



       Here follows a G98 job on a metal complex of Antimony (Sb)
   running DFT/B3LYP with a general basis set. The program seems
   to read properly all data set, however during the first SCF
   cycle it stops saying  


 Cycle   1  Pass 0  IDiag 1:
 Petite list used in FoFDir.
 MinBra= 0 MaxBra= 1 Meth= 1.
 IRaf=       0 NMat=   1 IRICut=       1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
 No pruned grid is available for atomic number  51.
 E=                  -nan
 DIIS: error=      nan at cycle   1.
 Logic error #1 in SortMO
 Error termination via Lnk1e in C:\G98W\l502.exe.


      Does anybody knows what should be done to fix it and have the 
  job done ? Thanks for the attention !


          Bye 
          Eduardo Hollauer 




     Below follows a short version of the output for those who
  want to have a look.

 *********************************************
 Gaussian 98:  x86-Win32-G98RevA.7 11-Apr-1999
                  30-Jun-2000 
 *********************************************
 %chk=sbdft.chk
 --------------------------------------------------------------------
 #P OPT DIRECT B3LYP/GEN GUESS=CARDS UNITS=AU PUNCH=MO PSEUDO=READ 6D
 --------------------------------------------------------------------
 1/14=-1,18=20,20=1,26=3,38=1/1,3;
 2/9=110,17=6,18=5/2;
 3/5=7,8=2,11=2,16=1,17=8,25=1,30=1/1,2,3;
 4/11=1,14=1/1;
 5/5=2,38=4,42=-5/2;
 6/7=2,8=2,9=2,10=2,28=1/1;
 7//1,2,3,16;
 1/14=-1,18=20/3(1);
 99/10=32/99;
 2/9=110/2;
 3/5=7,6=1,8=2,11=2,16=1,17=8,25=1,30=1/1,2,3;
 4/5=5,11=1,16=2/1;
 5/5=2,38=4,42=-5/2;
 7//1,2,3,16;
 1/14=-1,18=20/3(-5);
 2/9=110/2;
 6/7=2,8=2,9=2,10=2,19=2,28=1/1;
 99/9=1,10=32/99;
 Leave Link    1 at Fri Jun 30 17:13:28 2000, MaxMem=          0 cpu:       3.0
 (Enter C:\G98W\l101.exe)
 -----------
 G90 SBS10C6
 -----------
 ===================================================================================================================================
 PSEUDOPOTENTIAL PARAMETERS
 ===================================================================================================================================
  CENTER     ATOMIC      VALENCE      ANGULAR      POWER                                                       COORDINATES
  NUMBER     NUMBER     ELECTRONS     MOMENTUM     OF R      EXPONENT        COEFFICIENT                X           Y           Z
 ===================================================================================================================================
    1         16                                                                                   -2.830656 10.624639 -5.660577
                                   No pseudopotential on this center.
    2         16                                                                                    2.830656-10.624639 -5.660577
                                   No pseudopotential on this center.
    3          6                                                                                   -2.210748  8.441197 -3.378401
                                   No pseudopotential on this center.
    4          6                                                                                    2.210748 -8.441197 -3.378401
                                   No pseudopotential on this center.
    5         16                                                                                    0.856425  6.910905 -2.986283
                                   No pseudopotential on this center.
    6         16                                                                                   -0.856425 -6.910905 -2.986283
                                   No pseudopotential on this center.
    7         16                                                                                   -4.521328  7.351692 -1.071820
                                   No pseudopotential on this center.
    8         16                                                                                    4.521328 -7.351692 -1.071820
                                   No pseudopotential on this center.
    9          6                                                                                    0.000000  4.992206 -0.214280
                                   No pseudopotential on this center.
   10          6                                                                                    0.000000 -4.992206 -0.214280
                                   No pseudopotential on this center.
   11          6                                                                                   -2.418525  5.179625  0.663644
                                   No pseudopotential on this center.
   12          6                                                                                    2.418525 -5.179625  0.663644
                                   No pseudopotential on this center.
   13         16                                                                                    2.507882  2.947202  1.009160
                                   No pseudopotential on this center.
   14         16                                                                                   -2.507882 -2.947202  1.009160
                                   No pseudopotential on this center.
   15         16                                                                                   -3.756425  3.529269  3.358507
                                   No pseudopotential on this center.
   16         16                                                                                    3.756425 -3.529269  3.358507
                                   No pseudopotential on this center.
   17         51            5                                                                       0.000000  0.000000  4.046683
                                      F and up 
                                                     1       -2.9095100        0.75490000
                                                     1      -12.4492100        2.83072000
                                      S - F
                                                     0        5.8681900        7.55592000
                                                     2        1.1003600      -53.01395000
                                                     2        1.2179000       79.99053000
                                      P - F
                                                     0        3.5143000        8.30360000
                                                     2        0.8646100      -29.04708000
                                                     2        0.9602900       45.56610000
                                      D - F
                                                     0        2.4598100        9.22182000
                                                     2        0.7641500        7.92129000
 ===================================================================================================================================
 There are    96 symmetry adapted basis functions of A   symmetry.
 There are    96 symmetry adapted basis functions of B   symmetry.
 Initial guess orbital symmetries:
       Occupied  (A) (B) (B) (A) (A) (B) (A) (B) (B) (A) (A) (B)
                 (B) (A) (B) (A) (A) (B) (B) (A) (A) (B) (A) (B)
                 (B) (A) (B) (A) (B) (A) (B) (A) (B) (A) (B) (A)
                 (A) (B) (B) (A) (B) (A) (B) (A) (A) (B) (A) (B)
                 (B) (A) (B) (A) (A) (B) (B) (A) (A) (B) (A) (B)
                 (B) (A) (A) (B) (B) (A) (A) (B) (A) (B) (A) (B)
                 (A) (B) (A) (A) (B) (B) (A) (B) (A) (B) (A) (A)
                 (B) (B) (A) (B) (A) (B) (B) (A) (B) (A) (A) (B)
                 (A) (B) (A) (A) (B)
       Virtual   (A) (B) (B) (A) (B) (B) (A) (B) (A) (A) (B) (A)
                 (B) (A) (B) (A) (B) (A) (B) (A) (B) (A) (B) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (B) (B) (B)
                 (B) (B) (B) (B) (B) (B) (B) (B) (B) (B) (B) (B)
                 (B) (B) (B) (B) (B) (B) (B) (B) (B) (B) (B) (B)
                 (B) (B) (B) (B) (B) (B) (B)
 Leave Link  401 at Fri Jun 30 17:17:32 2000, MaxMem=    6291456 cpu:      95.0
 (Enter C:\G98W\l502.exe)
 IExCor= 402 DFT=T Ex=B+HF Corr=LYP ScaHFX= 0.2000
 ScaDFX=  0.8000  0.7200  1.0000  0.8100
 IRadAn=      0 IRanWt=     -1 IRanGd=            0 ICorTp=0
 Using DIIS extrapolation.
 Closed shell SCF:
 Requested convergence on RMS density matrix=1.00D-08 within  64 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Integral symmetry usage will be decided dynamically.
 IEnd=    125948 IEndB=    125948 NGot=   6291456 MDV=   6206789
 LenX=   6206789
 Fock matrices will be formed incrementally for  20 cycles.
 Integral accuracy reduced to 1.0D-05 until final iterations.

 Cycle   1  Pass 0  IDiag 1:
 Petite list used in FoFDir.
 MinBra= 0 MaxBra= 1 Meth= 1.
 IRaf=       0 NMat=   1 IRICut=       1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
 No pruned grid is available for atomic number  51.
 E=                  -nan
 DIIS: error=      nan at cycle   1.
 Logic error #1 in SortMO
 Error termination via Lnk1e in C:\G98W\l502.exe.
 Job cpu time:  0 days  0 hours 10 minutes  2.0 seconds.
 File lengths (MBytes):  RWF=   29 Int=    0 D2E=    0 Chk=    1 Scr=    1


From chemistry-request@server.ccl.net  Mon Jul 10 14:35:50 2000
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Date: Mon, 10 Jul 2000 20:36:15 +0200 (CEST)
From: Jochen Kuepper <Jochen@pc1.uni-duesseldorf.de>
To: AHMED MOHAMED EL-SHAFEI <amelsha@unity.ncsu.edu>
Cc: chemistry@ccl.net
Subject: CCL:Fortran Compiler for IRIX 6.2
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AHMED MOHAMED EL-SHAFEI writes:

 > Does any one know of any fortran Compiler web site for IRIX 6.2  free?
 > I was trying to install a fortran compiler  to get G94 running on a
 > silicon graphics machine, but I could not find any available free
 > downloadable Fortran Compiler!

http://gcc.gnu.org/

It might not help you with Gaussian, though ;-(
But then I don“t know.

Jochen
-- 
Heinrich-Heine-Universität, Institut für Physikalische Chemie I
Universitätsstr. 1, Geb. 26.43 Raum 02.29
40225 Düsseldorf, Germany                phone ++49-211-8113681
http://www.Jochen-Kuepper.de               fax ++49-211-8115195


